Fuses are changed in the boards.txt file.
Make up a new one for your specific board name if needed.
Put it and the pins_arduino.h on
/variants/new_board/ folder
Example:
bobuino.name=Bobuino
bobuino.upload.protocol=arduino
bobuino.upload.maximum_size=130048
bobuino.upload.speed=115200
bobuino.bootloader.low_fuses=0xff
bobuino.bootloader.high_fuses=0xde
bobuino.bootloader.extended_fuses=0xfd
bobuino.bootloader.path=Bobuino
bobuino.bootloader.file=AtmegaBOOT_1284P_16MHZ.hex
bobuino.bootloader.unlock_bits=0x3F
bobuino.bootloader.lock_bits=0x0F
bobuino.build.mcu=atmega1284p
bobuino.build.f_cpu=16000000L
#bobuino.build.core=arduino:arduino
bobuino.build.core=standard
bobuino.build.variant=bobuino